Systematic analysis of bZIP gene family in Suaeda australis reveal their roles under salt stress.

BACKGROUND: Suaeda australis is one of typical halophyte owing to high levels of salt tolerance. In addition, the bZIP gene family assumes pivotal functions in response to salt stress. However, there are little reports available regarding the bZIP gene family in S. australis. RESULTS: In this study, we successfully screened 44 bZIP genes within S. australis genome. Subsequently, we conducted an extensive analysis, encompassing investigations into chromosome location, gene structure, phylogenetic relationship, promoter region, conserved motif, and gene expression profile. The 44 bZIP genes were categorized into 12 distinct groups, exhibiting an uneven distribution among the 9 chromosomes of S. australis chromosomes, but one member (Sau23745) was mapped on unanchored scaffolds. Examination of cis-regulatory elements revealed that bZIP promoters were closely related to anaerobic induction, transcription start, and light responsiveness. Comparative transcriptome analysis between ST1 and ST2 samples identified 2,434 DEGs, which were significantly enriched in some primary biological pathways related to salt response-regulating signaling based on GO and KEGG enrichment analysis. Expression patterns analyses clearly discovered the role of several differently expressed SabZIPs, including Sau08107, Sau08911, Sau11415, Sau16575, and Sau19276, which showed higher expression levels in higher salt concentration than low concentration and a response to salt stress. These expression patterns were corroborated through RT-qPCR analysis. The six differentially expressed SabZIP genes, all localized in the nucleus, exhibited positive regulation involved in the salt stress response. SabZIP14, SabZIP26, and SabZIP36 proteins could bind to the promoter region of downstream salt stress-related genes and activate their expressions. CONCLUSIONS: Our findings offer valuable insights into the evolutionary trajectory of the bZIP gene family in S. australis and shed light on their roles in responding to salt stress. In addition to fundamental genomic information, these results would serve as a foundational framework for future investigations into the regulation of salt stress responses in S. australis.

The whole genome dataset of Ichthyscopus pollicaris.

The classification of the Uranoscopidae species is controversial and the Ichthyscopus pollicaris belonging to Uranoscopidae was first reported in 2019. In the present study, the whole genome sequence of I. pollicaris were generated by PacBio and Illumina platforms for the first time. After de novo assembly and correction of the high-quality PacBio data, a 527.25 Mb I. pollicaris genome with an N50 length of 11.25 Mb was finally generated. Meanwhile, 170.41 Mb repeating sequence, 21,263 genes, 784 miRNAs, 2,225 tRNAs, 3004 rRNAs, and 1422 snRNAs were annotated in I. pollicaris genome. Furthermore, 3,168 single-copy orthologous genes were applied to reconstructed the phylogenetic relationship between I. pollicaris and other 11 species. The draft genome sequences have been deposited in NCBI database with the accession number of PRJNA1071810.

Comparative transcriptome analysis reveals disruption of Plutella xylostella immune system by fungal peptide cyclosporin C.

The diamondback moth (Plutella xylostella), a major threat to crucifers across the globe, has developed resistance against the majority of insecticides enhancing the need for alternate control measures against this pest. Recently cyclosporin C, a secondary metabolite produced by the insect pathogenic fungus Purpeocillium lilacinum, has been reported to induce lethal and sub-lethal effects against P. xylostella. To date, little is known about the molecular mechanisms of interaction between cyclosporin C and P. xylostella immune systems. This study reports the transcriptome-based immune response of P. xylostella to cyclosprin C treatment. Our results showed differential expression of 322, 97, and 504 differentially expressed genes (DEGS) in P. xylostella treated with cyclosporin C compared to control 24, 48, and 72 h post-treatment, respectively. Thirteen DEGs were commonly expressed at different time intervals in P. xylostella larvae treated with cyclosporin C compared to control. Cyclosporin C treatment induced the down-regulated expression of majority of immune-related genes related to pattern recognition responses, signal modulation, Toll and IMD pathways, antimicrobial peptides and antioxidant responses confirming the ability to suppress immune response of P. xylostella. These results will further improve our knowledge of the infection mechanism and complex biochemical processes involved in interaction between cyclosporin C and insect immune systems.

An improved chromosome-level genome assembly and annotation of Echeneis naucrates.

Echeneis naucrates, as known as live sharksucker, is famous for the behavior of attaching to hosts using a highly modified dorsal fin with oval-shaped sucking disc. Here, we generated an improved high-quality chromosome-level genome assembly of E. naucrates using Illumina short reads, PacBio long reads and Hi-C data. Our assembled genome spans 572.85 Mb with a contig N50 of 23.19 Mb and is positioned to 24 pseudo-chromosomes. Additionally, at least one telomere was identified for 23 out of 24 chromosomes. Furthermore, we identified a total of 22,161 protein-coding genes, of which 21,402 genes (96.9%) were annotated successfully with functions. The combination of ab initio predictions and Repbase-based searches revealed that 15.57% of the assembled E. naucrates genome was identified as repetitive sequences. The completeness of the genome assembly and the gene annotation were estimated to be 97.5% and 95.4% with BUSCO analyses. This work enhances the utility of the live sharksucker genome and provides a valuable groundwork for the future study of genomics, biology and adaptive evolution in this species.

The first chromosomal-level genome assembly and annotation of white suckerfish Remora albescens.

Remora albescens, also known as white suckerfish, recognized for its distinctive suction-cup attachment behavior and medicinal significance. In this study, we produced a high-quality chromosome-level genome assembly of R. albescens through the integration of 23.87 Gb PacBio long reads, 64.54 Gb T7 short reads, and 88.63 Gb Hi-C data. Initially, we constructed a contig-level genome assembly totaling 605.30 Mb with a contig N50 of 23.12 Mb. Subsequently, employing Hi-C technology, approximately 99.68% (603.38 Mb) of the contig-level genome was successfully assigned to 23 pseudo-chromosomes. Through the integration of homologous-based predictions, ab initio predictions, and RNA-sequencing methods, we successfully identified a comprehensive set of 22,445 protein-coding genes. Notably, 96.36% (21,629 genes) of these were effectively annotated with functional information. The genome assembly achieved an estimated completeness of 98.1% according to BUSCO analysis. This work promotes the applicability of the R. albescens genome, laying a solid foundation for future investigations into genomics, biology, and medicinal importance within this species.

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS.

Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10-6 to 8.77 × 10-6, respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources.

Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis.

The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.

Research on the assignment of elderly care service personnel with time window constraints.

As the population continues to age, there is a growing need for elderly care services. In China, home care is widely embraced as a preferred method of caring for the elderly, and it has a promising commercial outlook. The strategic allocation of Elderly Care Service Personnel (ECSP) is a crucial component of the operational procedures for home care services. By strategically assigning elderly service personnel, it is possible to enhance the satisfaction and simultaneously minimize expenses. The issue of rationalizing the assignment of ECSP in the face of restricted resources is a genuine challenge that requires a solution, given the many types of elderly service demands and the skill requirements and time limits of certain projects. This study presents a strategy for assigning personnel on an hourly basis, taking into account time frame limits. This method involves several steps. Firstly, it involves assessing the specific service needs of the elderly, including the required door-to-door service time, service level, and gender preferences. Secondly, it calculates the service satisfaction and service operation cost of the Home Care Service Platform (HCSP) separately. Finally, it constructs a multi-objective elderly service personnel assignment method. This method aims to minimize the ECSP 's travel time and wasted time, maximize the satisfaction of the elderly by considering priority levels and ECSP scores, and minimize the operation cost of the HCSP. A model is developed to assign ECSP for elderly individuals, with the goal of minimizing travel time and wasted time, maximizing elderly satisfaction by considering priority and service personnel rating, and minimizing operating costs for the HCSP. Additionally, if there are unserved elderly individuals, an optimized path model is constructed using a cross-modified genetic algorithm to obtain the optimal matching result. Ultimately, an arithmetic example is employed to demonstrate the practicality and efficiency of the strategy put forth in this research. The findings demonstrate that the model presented in this research possesses distinct advantages in comparison to other conventional models.

Clinical significance of the combined test of seven blood coagulation indexes, lipids and platelet agglutination on hypercoagulable state of blood in parturient women.

Objective: To investigate the value of the combined test of seven blood coagulation indexes, lipids and platelet agglutination on the evaluation of the hypercoagulable state of blood in parturient women. Methods: This is a retrospective study. Total 50 high risk parturient women who underwent an antenatal examination in Baoding Maternal and Child Health Hospital from June 2021 to January 2023 were selected as the observation group, while 50 normal parturient women who underwent antenatal examination without comorbidities and complications were randomly collected in a ratio of 1:1 as the control group. All subjects had venous blood drawn for testing of seven blood coagulation indexes, lipids and platelet agglutination before delivery, and their general data were recorded. Results: The activated partial thromboplastin time(APTT) in the observation group was lower than that in the control group, while thrombin time(TT) and D-dimer(DD) were both higher than those in the control group, with statistically significant differences(p<0.05); total cholesterol (TC) and triglyceride (TG) in the observation group were both higher than those in the control group, with statistically significant differences (p<0.05); adenosine diphosphate (ADP) and arachidonic acid (AA) in the observation group were both higher than those in the control group, with statistically significant differences (p<0.05). Moreover, the overall incidence of adverse pregnancy was higher in the observation group than in the control group, with a statistically significant difference (p<0.05). Conclusions: The combined test of seven blood coagulation indexes, lipids and platelet agglutination results in excellent performance in predicting and judging the presence or absence of the hypercoagulable state of blood in parturient women, with the combination of APTT+TT+DD+TG+ADP+AA being the preferred test.

Ferroptosis mediated by TNFSF9 interferes in acute ischaemic stroke reperfusion injury with the progression of acute ischaemic stroke.

In this study, we investigated the potential involvement of TNFSF9 in reperfusion injury associated with ferroptosis in acute ischaemic stroke patients, mouse models and BV2 microglia. We first examined TNFSF9 changes in peripheral blood from stroke patients with successful reperfusion, and constructed oxygen-glucose deprivation-reperfusion (OGD-R) on BV2 microglia, oxygen-glucose deprivation for 6 h followed by reoxygenation and re-glucose for 24 h, and appropriate over-expression or knockdown of TNFSF9 manipulation on BV2 cells and found that in the case of BV2 cells encountering OGD-R over-expression of TNFSF9 resulted in increased BV2 apoptosis. Still, the knockdown of TNFSF9 ameliorated apoptosis and ferroptosis. In an in vivo experiment, we constructed TNFSF9 over-expression or knockout mice by intracerebral injection of TNFSF9-OE or sh-TNFSF9 adenovirus. We performed the middle cerebral artery occlusion (MCAO) model on day four, 24 h after ligation of the proximal artery, for half an hour to recanalize. As luck would have it, over-expression of TNFSF9 resulted in increased brain infarct volumes, neurological function scores and abnormalities in TNFSF9-related TRAF1 and ferroptosis-related pathways, but knockdown of TNFSF9 improved brain infarcts in mice as well as reversing TNFSF9-related signalling pathways. In conclusion, our data provide the first evidence that TNFSF9 triggers microglia activation by activating the ferroptosis signalling pathway following ischaemic stroke, leading to brain injury and neurological deficits.

The functions of exosomes targeting astrocytes and astrocyte-derived exosomes targeting other cell types.

Astrocytes are the most abundant glial cells in the central nervous system; they participate in crucial biological processes, maintain brain structure, and regulate nervous system function. Exosomes are cell-derived extracellular vesicles containing various bioactive molecules including proteins, peptides, nucleotides, and lipids secreted from their cellular sources. Increasing evidence shows that exosomes participate in a communication network in the nervous system, in which astrocyte-derived exosomes play important roles. In this review, we have summarized the effects of exosomes targeting astrocytes and the astrocyte-derived exosomes targeting other cell types in the central nervous system. We also discuss the potential research directions of the exosome-based communication network in the nervous system. The exosome-based intercellular communication focused on astrocytes is of great significance to the biological and/or pathological processes in different conditions in the brain. New strategies may be developed for the diagnosis and treatment of neurological disorders by focusing on astrocytes as the central cells and utilizing exosomes as communication mediators.

Transcriptomic profiling reveals the immune response mechanism of the Thamnaconus modestus induced by the poly (I:C) and LPS.

Aquatic animals immune response to pathogenic is a hotspot and related to high-quality development of aquaculture industry and the conservation of fisheries resources. Thamnaconus modestus is an important commercial and economical species which is suffering from various pathogens but by now lack relevant research about revealing the immune response mechanism to the pathogens invasion. In the study, the polyriboinosinic polyribocytidylic acid [poly (I:C)] and Lipopolysaccharides (LPS), respective mimics of viral and bacterial infections, were used to demonstrate the immune response of the species via transcriptome analysis. The results showed that T. modestus had sensitive responses to the viral analog infection at 6 h and 48 h, and at 6 h, the first five major functional genes were NFKBIA, IL1B, JUN, IGH, FOS, and at 48 h, the genes were NFKBIA, IL1B, JUN, IGH, FOS. The genes IL1B, IRF3, PTGS2, THBS1 could helping the fish to fight against the bacterial infection in both the times. Similarly for the bacterial infection, the species had a sensitive response at 6 h, and the first five major functional genes were NFKBIA, JUN, FOS, L1B, GRIN2C. Our study provided an insight about the immune response mechanism of this species and demonstrated that if need for treatment of the virus and bacteria by the biotechnology, the artificial interferential time would be suggested before 6 h since the pathological features occur and the genes NFKBIA, JUN, IL1B, FOS, TRAF2, IL8, SOCS3, PTGS2 should be payed more attention.

Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae).

It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.

Transcriptional responses of liver and spleen in Lota lota to polyriboinosinic polyribocytidylic acid.

Introduction: The cultured Lota lota can meet the market demand in the context of the decline of wild resources, but the disease in the high-density culture process also deserves attention. Therefore, understanding the immune regulation mechanisms of L. lota will be the basis for obtaining high benefits in artificial culture. Methods: To explore the viral response mechanism of L. lota, RNA-seq was applied to identify the transcriptomic changes of the liver and spleen in L. lota by poly (I:C) stress. Results: The DEGs (liver: 2186 to 3123; spleen 1542 to 2622) and up-regulated genes (liver: 1231 to 1776; spleen 769 to 1502) in the liver and spleen increased with the prolongation (12h to 48h) of poly (I:C)-stimulation time. This means L. lota needs to mobilize more functional genes in response to longer periods of poly (I:C)-stimulation. Despite the responses of L. lota to poly (I:C) showed tissue-specificity, we hypothesized that both liver and spleen of L. lota can respond to poly (I:C) challenge may be through promoting apoptosis of DNA-damaged cells, increasing the activity of immune-enhancing enzymes, and increasing energy supply based on DEGs annotation information. Conclusions: Our results demonstrate the transcriptional responses of L. lota to poly (I:C)-stimulation, and these data provide the first resource on the genetic regulation mechanisms of L. lota against viruses. Furthermore, the present study can provide basic information for the prevention of viral diseases in L. lota artificial culture process.

Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations.

BACKGROUND: Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent. RESULTS: To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction. CONCLUSIONS: Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.

Genomic Structure and Molecular Characterization of Toll-like Receptors in Black Scraper Thamnaconus Modestus and Their Expression Response to Two Types of Pathogens.

The black scraper (Thamnaconus modestus) is an important commercial species in China. However, with the rapid expansion of aquaculture, the culture of this species faces substantial economic losses due to infectious diseases. Toll-like receptors (TLRs) recognize a wide range of pathogen-associated molecular patterns (PAMPs) and play a crucial role in disease resistance by initiating innate immune responses in the host. The genome of the black scraper comprises eight TLR members, which can be classified into five subfamilies based on evolutionary analysis. Moreover, the TmTLRs were identified on 6 out of the 20 chromosomes in the black scraper. The functional similarity within the same subfamilies is evident by conserved motifs and gene structures. The qRT-PCR experiments revealed diverse TmTLR expression patterns in the liver, intestine, spleen, head kidney, heart, and brain of black scrapers, with high expression levels observed in immune organs, suggesting that TmTLRs may participate in the regulation of immune mechanisms and other physiological functions in the black scraper. At least six TmTLRs showed significantly upregulated expression in response to poly (I: C) or lipopolysaccharide (LPS) stresses, thus indicating their potential roles in regulating abiotic stress responses. In conclusion, our findings not only provide a foundation for future research on the TLR gene family in the black scraper but also offer guidance for disease prevention and vaccine development.

TLR pathway signaling molecules in burbot (Lota lota): molecular characterization, basal expression, and their response to Poly(I:C).

Burbot (Lota lota), a fish species of economic and ecological significance found across northern hemisphere freshwater ecosystems, was the focus of this study. We characterized 19 Toll-like receptor (TLR) genes in burbot, tracing their expression patterns following pathogen exposure. TLR genes, crucial to the innate immune system, including TLR13-1/2/3, TLR2/2-2/2-3/2-4/2-5, and TLR22a/22b/22c/22d, were discovered to be tandemly repeated, signifying an evolution in the fish's immune system. Notably, different TLR subfamilies displayed tissue-specific expressions, with TLR1 primarily in spleen and head kidney, TLR13 in head kidney, trunk kidney, and heart, TLR22 in trunk kidney and liver, and TLR3 and TLR9 predominantly in spleen and head kidney, but also in trunk kidney. Further, we investigated the response of TLR genes in burbot to pathogen exposure using qRT-PCR. This involved measuring mRNA expressions of identified TLR genes in spleen and liver tissues after injecting Poly(I:C) to simulate a double-stranded RNA viral infection. The results revealed a time and tissue-specific expression pattern. Specifically, LoTLR3 reached peak expression in the spleen 12 h post-injection, declining thereafter, while TLR2 subfamily members only began expressing after 24 h. In the liver, activation of the TLR3-IRF7 and TLR3-IRF3 signaling pathways was noted. Integrating these results with transcriptomic data illuminated the pivotal role of TLR genes in the burbot's immune response. Such findings are vital in shaping future disease prevention and treatment strategies.

Spleen Transcriptome Profiling Reveals Divergent Immune Responses to LPS and Poly (I:C) Challenge in the Yellow Drum (Nibea albiflora).

The yellow drum (Nibea albiflora) is a marine teleost fish with strong disease resistance, yet the understanding of its immune response and key functional genes is fragmented. Here, RNA-Seq was used to investigate the regulation pathways and genes involved in the immune response to infection with lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (poly (I:C)) on the spleen of the yellow drum. There were fewer differentially expressed genes (DEGs) in the LPS-infected treatment group at either 6 or 48 h. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs were mainly significantly enriched in c5-branching dibasic acid metabolic and complement and coagulation cascades pathways. The yellow drum responded more strongly to poly (I:C) infection, with 185 and 521 DEGs obtained under 6 and 48 h treatments, respectively. These DEGs were significantly enriched in the Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, Jak-STAT signaling pathway, NOD-like signaling pathway, and cytokine-cytokine receptor interaction. The key functional genes in these pathways played important roles in the immune response and maintenance of immune system homeostasis in the yellow drum. Weighted gene co-expression network analysis (WGCNA) revealed several important hub genes. Although the functions of some genes have not been confirmed, our study still provides significant information for further investigation of the immune system of the yellow drum.

The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis.

Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic−Indo−West Pacific (EIP). The WA group included four species belonging to four genera: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic−Indo−West Pacific (EIP) group was a younger group. Within the studied species, the genera Collichthys and Larmichthys were the youngest lineages, and we do not suggest that Collichthys and Larmichthys should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.